Polyhydroxybutyrate polymerase

ABSTRACT

A method for controlling and modifying biopolymer synthesis by manipulation of the genetics and enzymology of synthesis of polyhydroxybutyrate (PHB) and polyhydroxyalkanoate (PHA) polyesters at the molecular level in procaryotic and eukaryotic cells, especially plants. Examples demonstrate the isolation, characterization, and expression of the genes involved in the production of PHB and PHA polymers. Genes encoding the enzymes in the PHB and PHA synthetic pathway (beta-ketothiolase, acetoacetyl-CoA reductase and PHB polymerase or PHA polymerase) from  Zoogloea ramigera  strain I-16-M,  Alcaligenes eutrophus, Nocardia salmonicolur , and  Psuedomonas olevarans  were identified or isolated and expressed in a non-PHB producing organism,  E. coli . Specific modifications to the polymers include variation in the chain length of the polymers and incorporation of different monomers into the polymers to produce co-polymers with different physical properties.

This is a continuation-in-part of U.S. Ser. No. 067,695 entitled “Methodfor Producing Novel Polyester Biopolymers” filed Jun. 29, 1987 by OliverP. Peoples and Anthony J. Sinskey.

The United States government has rights in this invention by virtue ofgrants from the National Institute of Health, Office of Naval Research,and National Science Foundation.

BACKGROUND OF THE INVENTION

Synthesis by bacteria has long been the only means for production ofmany of the more complex biopolymers. Only recently have pathways forthe synthesis of these polymers been determined. Much effort has goneinto the isolation of the various enzymes and cofactors involved inthese pathways. Regulation of their expression has largely beenempirical, i.e., the concentration of nutrients or other factors such asoxygen level have been altered and the effect on polymer production andcomposition measured.

In order to have control over the production of these complexbiopolymers, and to modify them in a specific fashion, it is necessaryto design a system for determining the chemical steps required for theirsynthesis; to isolate and characterize the proteins responsible forthese chemical steps; to isolate, sequence, and clone the genes encodingthese proteins; and to identify, characterize, and utilize themechanisms for regulation of the rate and level of the expression ofthese genes.

Polyhydroxybutyrate, a commercially useful complex biopolymer, is anintracellular reserve material produced by a large number of bacteria.Poly-beta-hydroxybutyrate (PHB), the polymeric ester ofD(−)-3-hydroxybutyrate, was first discovered in Bacillus megaterium in1925. Both the chemical and physical properties of this unique polyesterhave made it an attractive biomaterial for extensive study. PHB has avariety of potential applications, including utility as abiodegradable/thermoplastic material, as a source of chiral centers forthe organic synthesis of certain antibiotics, and as a matrix for drugdelivery and bone replacement. In vivo, the polymer is degradedinternally to hydroxybutyrate, a normal constituent of human blood.

The enzymatic synthesis of the hydrophobic crystalline PHB granules fromthe C₂ biosynthon acetyl-CoA has been studied in a number of bacteria.Three enzymes: beta ketothiolase, acetoacetyl-CoA reductase and PHBpolymerase, are involved in the conversion of acetyl-CoA to PHB.

Thiolases are ubiquitous enzymes which catalyze the synthesis andcleavage of carbon-carbon bonds and thus occupy a central role incellular metabolism. Different thiolase enzymes are involved interpenoid, steroid, macrolide and other biosynthetic pathways as well asthe degradation of fatty acids. In Z. ramigera, the condensation of twoacetyl-CoA groups to form acetoacetyl-CoA is catalyzed bybeta-ketothiolase. The acetoacetyl-CoA is then reduced by anNADP-specific reductase to form D(−)-beta-hydroxybutyryl-CoA, thesubstrate for PHB polymerase.

Beta-Ketothiolase (acetyl-CoA-CoA-C-acetyl-transferase, E.C. 2.3.1.9)has been studied in A. beijerinckii (Senior and Dawes, Biochem. J., 134,225-238 (1973)), A. eutrophus (Oeding and Schlegel, Biochem. J., 134,239-248 (1973)), Clostridium pasteurianum (Bernt and Schlegel, Arch.Microbiol., 103, 21-30 (1975)), and Z. ramigera (Nishimura et al., Arch.Microbiol., 116, 21-27 (1978)). The cloning and expression of the Z.ramigera acetoacetyl-CoA reductase genes was described in U.S. Ser. No.067,695. This gene was then used as a hybridization probe to isolate thereductase gene from other bacterial species, including Alcaligeneseutrophus and Nocardia.

The reductase involved in PHB biosynthesis in Z. ramigera isstereospecific for the D(−)-isomer of hydroxybutyryl-CoA and usesNADP(H) exclusively as a cofactor. The best characterizedAcetoacetyl-CoA reductase is that from Zoogloea, described by Saito etal., Arch. Microbiol. 114, 211-217 (1977) and Tomita et al.,Biochemistry of Metabolic Processes, 353, D. Lennon et al., editors(Elsevier, Holland, 1983). This NADP-specific 92,000 molecular weightenzyme has been purified by Fukui, et al., Biochim. Biophys. Acta 917,365-371 (1987) to homogeneity, although only in small quantities. Asdescribed in U.S. Ser. No. 067,695, the beta-ketothiolase enzyme from Z.ramigera has now been cloned, expressed and the product thereof purifiedto homogeneity. The cloned gene was used to identify and isolate thecorresponding beta-ketothiolase gene in other bacterial species,including Alcaligenes eutrophus and Nocardia.

The PHB polymerase in Z. ramigera is stereospecific forD-beta-hydroxybutyryl CoA. Synthetases from other bacteria such as A.eutrophus can utilize other substrates, for example,D-beta-hydroxyvaleryl CoA, since addition of propionate into A.eutrophus cultures leads to incorporation of C₅ and C₄ units into aPHB/HV copolymer. Griebel and Merrick, J. Bacteriol., 108, 782-789(1971) separated the PHB polymerase from native PHB granules of B.megaterium, losing all of the enzyme activity in the process. They wereable to reconstitute activity only by adding PHB granules to one of twofractions of the protein. More recently, Fukui et al., Arch. Microbiol.,110, 149-156 (1976) and Tomita et al. (1983), investigated this enzymein Z. ramigera and partially purified the non-granule bound PHBpolymerase. A method for cloning, expressing and using the productthereof in the synthesis of novel polymers was described in U.S. Ser.No. 067,695.

A whole range of polyhydroxalkanoate (PHA) storage polymers has beenfound to be produced by bacteria, including A. eutrophus and P.oleovarans. The PHA polymers are heteropolymers of the D-isomer of8-hydroxyalkanoates with the variation occurring in the length of theside chains (CH₃—CH₈H₁₇). For example, when grown in the presence of5-chloropentanoic acid, A. eutrophus incorporates 3-hydroxybutyrate,3-hydroxyvalerate and 5-hydroxyvalerate into the polymer.

Given the extremely high yields of this polymer obtainable throughclassic fermentation techniques, and the fact that PHB and PHA ofmolecular weight greater than 10,000 is useful for multipleapplications, it is desirable to develop new PHB-like biopolymers toimprove or create new applications.

The production of poly-beta-hydroxyalkanoates, other than PHB, bymonocultures of A. eutrophus and Pseudomonas oleovorans was reported bydeSmet, et al., in J. Bacteriol. 154, 870-878 (1983). In both bacteria,the polymers were produced by controlled fermentation. A. eutrophus,when grown on glucose and propionate, produces a heteropolymer ofPHB-PHV, the PHV content reaching approximately 30%. P. oleovoransproduces a homopolymer of poly-beta-hydroxyoctanoate when grown onoctane. Nocardia has been reported to form copolymers ofPHB-PH-2-butenoate when grown on n-butane. Determination of the finalcomposition of 3-hydroxybutyrate polymers by controlled fermentationusing selected substrates is also disclosed in U.S. Pat. No. 4,477,654to Holmes et al.

With the availability of a variety of enzymes varying as to theirsubstrate specificity and techniques for expressing the genes encodingthe enzymes in other hosts, especially plants, it is possible to providean economic, biodegradable alternative to the presently availableplastics derived from petroleum, especially polypropylene.

It is therefore an object of the present invention to provide furtherenzymes for use in a method for synthesis of complex biopolymers,particularly PHB, PHA and similar polymers.

It is a further object of this invention to isolate, sequence, and cloneadditional genes encoding these proteins for polymer synthesis, as wellas means for regulation of the rate and level of the expression of thesegenes.

It is another object of the present invention to provide purifiedproteins expressed from the genes encoding the proteins for synthesis ofpolyhydroxybutyrate and polyhydroxyalkanoate.

It is a further object of the present invention to provide methods forusing these proteins and regulatory sequences to create novelbiopolymers having polyester backbones.

It is a still further object of the present invention to provide aneconomic source of biodegradable polyhydroxyalkanoates and novel relatedpolymers, using both bacterial and plant cells for production.

SUMMARY OF THE INVENTION

A method for controlling and modifying biopolymer synthesis bymanipulation of the genetics and enzymology of synthesis ofpolyhydroxybutyrate (PHB) and polyhydroxyalkanoate (PHA) polyesters atthe molecular level in procaryotic and eukaryotic cells, especiallyplants.

Examples demonstrate the isolation, characterization, and expression ofthe genes involved in the production of PHB and PHA polymers. Genesencoding the enzymes in the PHB and PHA synthetic pathway(beta-ketothiolase, acetoacetyl-CoA reductase and PHB polymerase or PHApolymerase) from Zoogloea ramigera strain I-16-M, Alcaligenes eutrophus,Nocardia salmonicolur, and Psuedomonas olevarans were identified orisolated and expressed in a non-PHB producing organism, E. coli.

In a preferred embodiment using bacterial cells, the polymer is made inA. eutrophus due its capacity for accumulating PHB up to 70 to 80% drycell weight under conditions of nitrogen or phosphate limitation. Inanother embodiment, the genes are introduced into plant cells forexpression and synthesis of PHB, PHA, and novel polymers. Specificmodifications to the polymers include variation in the chain length ofthe polymers and incorporation of different monomers into the polymersto produce co-polymers with different physical properties.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 is the thiolase gene sequence from Zoogloea ramigera. Thesequences located at positions homologous to the E. coli “−10” and “−35”concensus regions (−100 to −95 and −122 and −116) upstream from thetranscription start site (bold arrow) are underlined. A probableribosome binding site is underlined (−11 to −8).

FIG. 2 is the complete nucleotide sequence of 2.3 kb of Z. ramigera DNAlocated downstream from the thiolase gene in clone pUCDBK1, encoding theacetoacetyl CoA reductase. The sequence of 2094 bp extending from thefirst Sal1 site to the second Sma1 site is shown. Also shown is thetranslation product of the acetoacetyl-CoA reductase structural geneextending from the ATG at nucleotide 37 to the TGA stop codon atnucleotide 760. Boxed amino acid residues 2 to 6 are identical to thoseobtained by Edman degradation of the purified protein. A potentialribosome binding site is underlined and a potential transcriptionterminator is indicated by arrows. Restriction sites for Sal1 and Sma1are shown.

FIG. 3 shows the nucleotide sequence of a corresponding 2 kb fragment A.eutrophus DNA cloned in plasmid pAeT3. The translation products of theA. eutrophus thiolase and acetoacetyl-CoA reductase genes extending fromnucleotides 40 to 1219 and 1296 to 2034, respectively, are shown.Restriction endonuclease cleavage sites used in the construction of theoverproduction vectors pAT and pAR are shown. Pst 1=Pst 1; Ava=2 andDde=Dde 1.

FIG. 4 is the nucleotide sequence of the PHB polymerase (phbC) locus ofAlcaligenes eutrophus H16. The translation product of the open readingframe from position 842 to position 2608, the predicted amino acidsequence of PHB polymerase is shown. Also shown is the translationproduct of the first 72 nucleotides of the phbA gene. A sequence capableof forming a hairpin structure (position 2660) is indicated by thearrows.

FIG. 5 shows the potential coding regions of the P. oleovarans PHApolymerase gene, open reading frames ORF1, ORF2, and ORF3. ORF1 beginsat the ATG initiation codon nucleotide 554 and ends at the TGA stopcodon nucleotide 2231 and encodes a polypeptide of 562 amino acids withan M_(r)=60,000. ORF2 begins at the ATG position 2297 and ends at theTAA position 3146. ORF2 begins at the ATG position 3217 and ends at theTGA position 4948.

FIG. 6 is the nucleotide sequence analysis of the complete 6 kb fragmentcontaining the P. oleovarans phbC gene.

DETAILED DESCRIPTION OF THE INVENTION

The following methods were used to isolate genes encoding beta-ketothiolase, acetoacetyl-CoA reductase, PHB polymerase, and PHA polymerase,and their expression products, to identify and characterize sequencesregulating their expression, and to determine the effect of cultureconditions and substrate availability oh polymer production. Techniquesfor constructing systems for the production of PHB and PHA-likebiopolymers are also disclosed. By combining these enzymes in eitherbacterial or plant cells with the appropriate substrates undercontrolled culture conditions of available oxygen and temperature, avariety of polymers can be constructed. The enzymes or nucleotidesequences controlling their expression can also be modified to alter thequantity of expression or substrate specificity to further vary theresulting polymers. An added advantage is that substrates which normallycannot be used with whole cells can be manufactured using the isolatedenzymes.

The methods, genes, and products of their expression and polymersynthesis are described in detail in the following non-limitingexamples.

Media and Culture Conditions.

Zoogloea ramigera strain I-16M (ATCC 19623) was used initially to studythe genetics of the PHB biosynthetic pathway. Z. ramigera DNA waspurified from 200 ml mid-log phase cultures as follows: cells wereharvested by centrifugation, washed in 20 mM Tris-HCl, pH 8.2, andresuspended in 10 ml of Tris-HCl. The cells were then spheroplasted bythe addition of 10 ml of 24% w/v polyethylene glycol 8000 and 2 ml of 25mg/ml lysozyme, followed by incubation at 37° C. for 30 min. Thespheroplasts were harvested by centrifugation, resuspended in 5 ml of TEbuffer (10 mM Tris-HCl, pH 8.0, 1 mM EDTA), 300 microliters of 10% w/vSDS added, and the cells lysed by incubating at 55° C. for 10 min. Anadditional 10 ml of TE was added and the lysate incubated with RNAse (50microgram/ml) and proteinase K (30 microgram/ml) for 1 h at 37° C. TheDNA was then purified by CsCl gradient centrifugation.

E. coli strains were grown in LB (Luria Bertani) medium, (NaCl, 10 g/l;Tryptone, 10 g/l; yeast extract, 10 g/l) or 2×TY medium (NaCl, 5 g/l;Tryptone, 16 g/l; yeast extract, 10 g/l). For the production of PHB orPHA by E. coli containing recombinant plasmids, minimal media was used,with the modification that the (NH₄)₂SO₄ concentration was decreased to0.04%.

A. eutrophus strains were grown in Trypticase soy broth (TSB, BBLMicrobiology systems, Cockeysville, Md.) or a defined minimal mediumcomposed of. 0.39 g/1 MgSO₄; 0.45 g/l K₂SO₄; 12 ml 1.1 m H₃PO₄; 15 mg/lFeSO₄.7H₂O; 24 ml trace elements (20 mg/l CuSO₄.5H₂O; 100 mg/lZnSO₄.6H₂O; 100 mg/l MnSO₄4H₂O; 2.6 g/l CaCl₂₂H₂O). The pH was adjustedto 6.8 with NaOH and the medium sterilized by autoclaving. NH₄Cl wasadded to a final concentration of 0.1% or 0.01% as nitrogen source andfructose was added to a final concentration of 0.5-1% (w/v).

Plasmid DNA preparations were carried out using the method of Birnboimand Doly in Nucleic Acids Res., 7, 1513-1523(1979) as described byIsh-Horowicz and Burke, Nucleic Acids Res., 9, 2989-2998 (1981). LambdaDNA was prepared by standard procedures described in Maniatis et al.,Molecular Cloning: A Laboratory Manual. (Cold Spring Harbor Laboratory,Cold Spring Harbor, N.Y. 1982). DNA sequence analysis was carried outusing the M13 mp18 and M13 mp19 cloning vectors (Yanisch-Perron, et al.,Gene 33,103-109 (1985)) and the dideoxy chain termination procedure ofSanger, et al., Proc. Natl. Acad. Sci. USA 74, 5463-5467 (1977).α-[³⁵S]-dATP and the Klenow fragment of DNA polymerase 1 were purchasedfrom Amersham. Sequence data were compiled and analysed on a VAX system.

A recombinant library of random Z. ramigera chromosomal DNA fragmentswas constructed using the lambda gt11 expression vector described byYoung and Davis, Science, 222, 778-782 (1983). Z. ramigera DNA was firstmethylated using EcoRI methylase and then partially digested with DNAse1 in the presence of Mg²⁺, as taught by Anderson, Nucleic Acids, 9,3015-3026 (1981). The ends of the partially digested DNA fragments wererepaired using Klenow polymerase, EcoRI linkers added, and the DNAdigested to completion with an excess of EcoRI. Fragments of 2-8 kb weresize-selected on a 1.5% agarose gel, purified by electroelution, andligated with EcoRI-digested phosphatased lambda gt11 DNA. Ligations werecarried out for 18 h at 4° C. using 2 micrograms of lambda gt11 DNA and1 microgram of fragmented chromosomal DNA in a total volume of 10microliters. The complete ligation reactions were packaged in vitrousing lambda extracts prepared from E. coli strains BHB2688 and BHB2690,Hohn and Murray, Proc. Natl. Acad. Sci., USA, 74, 3259-3263 (1977), asdescribed by Maniatis et al. (1982). Packaged phage were plated out andamplified on E. coli Y1088.

Screening of the lambda gt11 expression library was carried out usingrabbit anti-thiolase antibodies and a modification of the proceduredescribed by Young and Davis, Science, 222, 778-782 (1983).

Restriction endonucleases, T4 DNA ligase and DNA polymerase 1 wereobtained from New England Biolabs and used under conditions provided bythe manufacturer. Calf intestinal alkaline phosphatase was purchasedfrom Boehringer Mannheim Corporation. All routine DNA manipulations,including plasmid purifications, E. coli transformations, etc. wereperformed using methods described by Maniatis, et al. (1982).Chromosomal DNA was purified from A. eutrophus strains, grown to latelogarithmic phase in TSB. Transfer of restriction digested DNA samplesfrom agarose gels to nitrocellulose filters, prehybridization andhybridization with ³²P-labelled DNA probes was as described by Peoples,et al., J. Biol. Chem. 262, 97-102 (1987). Rapid plasmid isolation fromA. eutrophus recombinant strains for restriction analysis were performedby the alkaline extraction procedure of Birnboim and Doly, Nucleic AcidsRes. 7, 1513-1523 (1979).

Conjugation in A. eutrophus.

The conjugal transfer of the broad host range plasmid, pLAFR3, orrecombinant derivatives of pLAFR3, into A. eutrophus was performed usingthe method described by Easson et al, J. Bacteriol. 169, 4518-4524(1987). In this case, however, the recipient A. eutrophus cells were notsonicated and transconjugants were selected on A. eutrophus mineral agarplates containing 0.01% NH₄Cl as nitrogen source, 1% (w/v) fructose ascarbon source and 10 μg/ml tetracycline.

For Tn5 mutagenesis, a spontaneous streptomycin resistant strain of A.eutrophus 11599 (1599 S1) was used. Transfer of pRK602 (Tn5) was carriedout as described above using E. coli MM294A (pRK602) as the only donor.A. eutrophus strains containing Tn5 were selected for by growth onstreptomycin (500 μg/ml) and kanamycin (100 μg/ml).

Identification of the Z. ramigera Thiolase gene.

Thiolase antiserum was prepared in New Zealand White female rabbits,using purified thiolase protein by standard procedures. Antibody titerwas estimated by the Ouchterlony double-diffusion assay, Acta Pathol.Microbiol. Scand. 26, 507-515(1949). Purified antibody was prepared fromthe serum by chromatography on protein A agarose according to Bighee etal., Mol. Immunol. 20, 1353-1357 (1983). Approximately 4×10⁴ recombinantphage adsorbed to E. coli Y1090 were plated out on 15 cm LB-agar platesand incubated at 42° C. for 3 h. The plates were then overlayed withnitrocellulose filters (Schleicher & Schull, BA85), which had previouslybeen saturated in 10 mM IPTG, and incubated a further 4 h at 37° C.Filters were removed, washed for 10 min in TBST (50 mM Tris-HCl, pH 7.9,150 mM NaCl, 0.05% Tween-20), incubated in TBST plus 20% v/v fetal calfserum for 30 min, and rinsed in TBST. First antibody was bound byincubating the filters in 10 ml TBST plus purified anti-thiolaseantibody (10 microliters) for 1 h at room temperature. The filters weresubsequently washed in three changes of TBST for 5 min each time. Boundfirst antibody was detected using a biotin-avidin horseradish peroxidasedetection system (Clontech Laboratories) and horseradish peroxidasecolor development reagent (Bio-Rad Laboratories, Richmond, Va.).

Proteins were separated by sodium dodecyl sulphate-polyacrylamide gelelectrophoresis according to the method of Laemmli, Nature 222, 680-685(1970) and electrophoretically transferred to nitrocellulose filters(Schleicher & Schuill BA85), essentially as described by Burnette, Anal.Biochem. 112, 195-203 (1981). Following transfer overnight at 30 V,filters were rinsed in TBS (TBST without Tween-20) and incubated in TBSplus 5% bovine serum albumin. Proteins reacting with anti-thiolase serumwere then detected by incubating the filters in 100 ml of TBS, 1%gelatin containing 2 ml of anti-thiolase serum for 1-2 h. Bound firstantibody was subsequently detected using goat anti-rabbit IgGhorseradish peroxidase conjugate and horseradish peroxidase colordevelopment reagent (Bio-Rad Laboratories, Richmond, Calif.).

DNA blots were prepared using DNA fragments separated on agarose gels bythe sandwich blot method of Smith and Summers, Anal. Biochem. 109,123-129 (1980) based on the technique developed by Southern, J. Mol.Biol. 98, 503-517 (1975). Filters were hybridized with DNA probeslabeled to a high specific activity (0.1-1×10⁸ cpm/μg of DNA) with[α-³²P]dATP, by nick translation, Rigby et al., J. Mol. Biol., 113,237-251 (1977). Prehybridizations and hybridizations were carried out at65° C. in sealed polythene bags. The prehybridization/hybridizationsolution contained 5×SSCP (1×SSCP contains 0.15 M NaCl, 0.15 M sodiumcitrate, 10 mM Na₂HPO₄, 10 mM NaH₂PO₄), 5× Denhardt's solution, 0.1%(w/v) SDS, 10 mM EDTA, and 100 μg/ml sonicated denatured salmon DNA.Filters were prehybridized for 8-18 h and hybridized for 16-18 h using10⁷ cpm of labeled DNA probe per filter.

Lysogens of lambda gt11 recombinant clones were prepared in E. coliY1089 as described by Young and Davis, Science 222, 778-782 (1983). Forthe preparation and analysis of lambda-coded proteins, lysogens weregrown at 30° C. in LB (100 ml) until they reached an OD₆₀₀ of 0.5. Theprophage was induced by a 20 min incubation at 45° C., IPTG added to 5mM and the induced lysogens incubated at 37° C. for 1 h. Cells wereharvested, resuspended in assay buffer (0.1 M Tris-HCl, pH 7.5, 5 mMbeta-mercaptoethanol, 5% (v/v) glycerol), lysed by sonication, celldebris pelleted by centrifugation, and the cell extracts stored at −20°C. The protein concentrations of bacterial lysates were assayed by themethod of M. M. Bradford in Anal. Biochem. 72, 248-254 (1976), usingbovine serum albumin as a standard. Thiolase-enzyme assays wereperformed as described by Nishimura, et al., Arch. Microbiol. 116, 21-27(1978).

DNA fragments were cloned into the M13 vectors mp10 and mp11 andsequenced by the dideoxy chain-termination method of Sanger et al.,Nucleic Acids Res. 10, 141-158 (1980), Proc. Natl. Acad. Sci. USA 74,5463-5467 (1977). The M13 sequencing primer and other reagents werepurchased from Amersham Corp. G/C rich regions were resequenced usingdITP in place of dGTP as described by Mills and Kramer, Proc. Natl.Acad. Sci. USA 76, 2232-2235 (1979). Computer-assisted sequence analysiswas accomplished using the Staden programs. Acids Res. 10, 141-158(1984).

Approximately 2×10⁵ recombinants were obtained from 1 μg of purifiedtarget DNA, and amplified in E. coli Y1088. A total of 10⁵ amplifiedphage were screened using purified rabbit anti-thiolase antibodies. Theinitial screening identified 10 potentially positive clones(LDBK1-LDBK10). Analysis by restriction digestions demonstrated thatclones LDBK2-10 are identical. Clones LDBK1 and LDBK2 were selected forfurther study. LDBK1 has an insert composed of 2 EcoRI fragments of 3.6kb and 0.75 kb. LDBK2 has an insert composed of 3 EcoRI fragments of1.65 kb and 1.08 kb.

The proteins coded for by the LDBK1 and LDBK2 insert sequences wereanalyzed both for thiolase-enzyme activity and for cross-reaction torabbit anti-thiolase serum. Lysogenic strains of E. coli Y1089containing LDBK1 and LDBK2 phage DNA were prepared. Several lysogenswere obtained for each clone and two of these, Y1089/LDBK1 andY1089/LDBK2, were used for subsequent studies. A lysogen of the lambdagt11 vector, BNN97/lambda gt11, was used as a control. The results ofthe thiolase-enzyme assays clearly indicate that the proteins fromY1089/LDBK1 contain a substantial amount of thiolase activity.Furthermore, the thiolase activity is inducible, greater than 5-fold, bythe addition of IPTG. This shows that expression of the thiolase-codingsequences is under the transcriptional control of the lac promotercontained in the lambda gt11 vector. Neither the Y1089/LDBK2 nor theBNN97/lambda gt11 protein lysates demonstrate any significantthiolase-enzyme activity even when induced with IPTG.

The size of the proteins responsible for the initial positive reactionto rabbit anti-thiolase antibodies was investigated by Western blotexperiments. Protein lysates were separated by SDS-polyacrylamide gelelectrophoresis, transferred to nitrocellulose filters, and screenedwith rabbit anti-thiolase serum. The results show an immunoreactive40,000 dalton protein in both the IPTG-induced and non-IPTG-inducedlysate of Y1089/LDBK1.

The LDBK1 insert was restriction mapped. The large 3.6 kb EcoRIfragment, containing the complete thiolase gene region, was subclonedinto the plasmid vector pUC8 for ease of manipulation. Restrictionanalysis of one of the subclones obtained, pUCDKB1, confirmed therestriction map of this fragment in LDBK1. pUCDBK1 DNA was labeled to ahigh specific activity with ³²P and hybridized to nitrocellulose filterscontaining Z. ramigera chromosomal DNA digested with the same enzymesused to restriction map pUCDBK1. Southern hybridization experimentsconfirm that the 5.4 kb genomic fragment hybridizes to both a 1.45 kbSalI/EcoRI and 1.05 kb SalI fragment from pUCDBK1. Based on the resultof Southern hybridization experiment, the cloned pUCDBK1 insert isrepresented in the Z. ramipera genome only once.

DNA sequence analysis of the pUCDBK1 insert was carried out using theM13/Sanger dideoxy chain termination method. To locate the gene-codingregion, individual DNA sequences were scanned in all six reading framesfor homology to the NH₂-terminal amino acid sequence. By using thisapproach, the gene-coding region within the 1.45 kb EcoRI/SalI fragmentwas identified. The complete nucleotide sequence of the plus strand ofthe gene is shown in FIG. 1. 290 bp downstream from the EcoRI site liesthe start of the thiolase structural gene, assigned by comparing the DNAsequence to the NH₂-terminal amino acid sequence. The NH₂-terminalsequence lies in the single long open reading frame which extends fromposition −89 to the stop codon (TAG) at nucleotide 1174. Beginning witha serine and extending for 25 residues, the experimentally determinedNH₂-terminal sequence aligns identically with residues 2 through 26 ofthe translated DNA sequence. Translation of the DNA sequence was thenused to deduce the remaining amino acid sequence from residue 27 to 391(nucleotides 79 to 1173). Hence, translation of the DNA sequence fromnucleotide 1 to 1174 (in this reading frame) encodes a 391-amino acidpolypeptide with a calculated M_(r) of 40,598. This value is in verygood agreement with that of M_(r)=42,000 determined bySDS-polyacrylamide gel electrophoresis.

Two additional pieces of evidence confirm that this translation produceis the correct amino acid sequence of thiolase. First, a search of thepredicted amino acid sequence for the active site peptide(NH2-Gly-Met-Asn-Gln-Leu-Cys-Gly-Ser-Gly-COOH) located this peptide atresidues 84-92. Finally, the predicted amino acid composition from thetranslation product and that determined experimentally are in excellentagreement. The GIC content of the 1.46 kb EcoRI-SalI fragment is high,66.2%. When considered separately, the 5′-flanking 290 bp has a G/Ccontent of 57.4% and the structural gene region 68.4%. The amino acidsequence confirms that the Z. ramigera thiolase contains 5 cysteineresidues. The Z. ramigera active site cysteine is at residue Cys-89.Additional cysteines which may be involved in inter- or intradisulphidebonds are Cys-125, Cys-323, Cys-377, and Cys-387. NH₂-terminal sequenceanalysis indicated a serine at position 1.

Seven nucleotides upstream from the ATG start codon is a potentialribosome-binding site, 5′-CTGAGGA-3′, identified by homology to the E.coli sequence. Additional start codons including two GTGs which caninitiate translation in some bacterial genes are located furtherupstream. Examination of the 5′-flanking region for homology to the“−10” and “−35” E. coli promoter elements, identified a potential “−35′region at residues −122 to −116 and a corresponding “−10 region”,5′-TATAAT-3′, at position −100 to −95. A poly(T) tract at position −255to −266 is also present. It is clear that the only post-translationalprocessing of thiolase is the removal of the N-formylmethionine residue,as alternate start codons, ATC or GTG, are either out of frame or havean in-frame stop codon before the start of the structural gene.

The 1.5 Kb Sal1-EcoR1 fragment from pUCDBK1 contains the entire Z.ramigera thiolase structural gene plus 283 bp of 5′/flanking DNA. Aseries of plasmid constructions were made in which this DNA fragment wasinserted into the tac promoter vector pKK223-3 (or derivatives thereof).pZT3 was made by cleaving pUCKBK1 with Sal1, blunt-ending with Klenowpolymerase and adding on EcoR1 linkers. Following digestion with EcoR1,the 1.5 Kb fragment was purified from an agarose gel and inserted intothe EcoR1 site of pKK223-3. Recombinant clones having the gene insertedin the correct orientation with respect to the tac promoter wereidentified by restriction analysis following transformation of E. coliJM105.

A series of clones deleted of sequences in the 283 bp flanking the 5′end of the thiolase gene was then constructed. pUCDBK1 DNA was digestedwith EcoR1 and treated with Bal31 nuclease. Following Sal1 digestion,the ends of the fragments were repaired with Klenow and EcoR1 linkersadded on. The plasmid DNA was cleaved with EcoR1 and fragments in thecorrect size range, 1.2-1.4 kb, purified from an agarose gel and ligatedinto the EcoR1 site of pKK223-3. Clones of interest were identified byrestriction mapping and the extent of the 5′-deletion determined by DNAsequencing. From this series of clones, pZT3.1-pZT3.5, the clone withthe largest deletion, pZT3.5, had 84 bp of the 5′-flanking DNA remainingand therefore a subsequent Bal31 deletion experiment was carried out asfollows: pZT3.5 DNA was digested to completion with EcoR1 and treatedwith Bal31 nuclease; the ends were repaired using Klenow polymerase andEcoRI linkers ligated on, following digestion to completion with EcoR1and BamH1, fragments corresponding to the NH₂-terminal region ofthiolase were eluted from an agarose gel, ligated with BamH1-EcoR1digested M13 mp 11 DNA and plated out on E. coli JM101; single-strandedDNA was prepared from 50 transformants and the extent of the 5′-deletionanalyzed by T-tracking; double-stranded DNA was prepared, in vitro, fromclones of interest and the EcoR1-Bam1 inserts recovered by restrictiondigestion and elution from an agarose gel.

In order to reconstruct the intact thiolase gene, the 290 bpBamH1-HindIII fragment from pZT3.5 was ligated into a vector (pKK226)derived from pKK223-3 by deleting the BamH1 site upstream from the tacpromoter; this C-terminal vector was subsequently used for thereconstruction of the Bal31 deleted NH₂-termini of interest; clonespZT3.5.1 and pZT3.5.2 were used in subsequent studies.

The effect of deleting sequences in the 283 bp of DNA flanking thethiolase ATG translation initiation codon was determined by analyzingthe level of thiolase activity produced by plasmids pZT3.1-pZT3.5.2. 100ml cultures of the E. coli JM105 containing each plasmid were inducedwith IPTG for 15 hours and the level of thiolase assayed. The mostnotable feature of these results is the very high level of thiolaseexpression obtained with clones pZT3.3-pZT3.5.2, the maximum obtainedbeing 178 U/mg for pZT3.5. This represents an increase of 5.9-fold ascompared to plasmid pZT3 which contains the entire 283 bp of 5′-flankingDNA. The data demonstrate that the thiolase 5′-flanking sequenceslocated between −84 (pZT3.5) and −168 (pZT3.2) strongly inhibit theexpression of the thiolase gene from the tac promoter. The location ofthese sequences can be narrowed down to the region between −84 (pZT3.5)and −124 (pZT3.4) as the deletion of was ligated into a vector (pKK226)derived from pKK223-3 by deleting the BamH1 site upstream from the tacpromoter; this C-terminal vector was subsequently used for thereconstruction of the Bal31 deleted NH₂-termini of interest; clonespZT3.5.1 and pZT3.5.2 were used in subsequent studies.

The effect of deleting sequences in the 283 bp of DNA flanking thethiolase ATG translation initiation codon was determined by analyzingthe level of thiolase activity produced by plasmids pZT3.1-pZT3.5.2. 100ml cultures of the E. coli JM105 containing each plasmid were inducedwith IPTG for 15 hours and the level of thiolase assayed. The mostnotable feature of these results is the very high level of thiolaseexpression obtained with clones pZT3.3-pZT3.5.2, the maximum obtainedbeing 178 U/mg for pZT3.5. This represents an increase of 5.9-fold ascompared to plasmid pZT3 which contains the entire 283 bp of 5′-flankingDNA. The data demonstrate that the thiolase 5′-flanking sequenceslocated between −84 (pZT3.5) and −168 (pZT3.2) strongly inhibit theexpression of the thiolase gene from the tac promoter. The location ofthese sequences can be narrowed down to the region between −84 (pZT3.5)and −124 (pZT3.4) as the deletion of was ligated into a vector (pKK226)derived from pKK223-3 by deleting the BamH1 site upstream from the tacpromoter; this C-terminal vector was subsequently used for thereconstruction of the Bal31 deleted NH₂-termini of interest; clonespZT3.5.1 and pZT3.5.2 were used in subsequent studies.

The effect of deleting sequences in the 283 bp of DNA flanking thethiolase ATG translation initiation codon was determined by analyzingthe level of thiolase activity produced by plasmids pZT3.1-pZT3.5.2. 100ml cultures of the E. coli JM105 containing each plasmid were inducedwith IPTG for 15 hours and the level of thiolase assayed. The mostnotable feature of these results is the very high level of thiolaseexpression obtained with clones pZT3.3-pZT3.5.2, the maximum obtainedbeing 178 U/mg for pZT3.5. This represents an increase of 5.9-fold ascompared to plasmid pZT3 which contains the entire 283 bp of 5′-flankingDNA. The data demonstrate that the thiolase 5′-flanking sequenceslocated between −84 (pZT3.5) and −168 (pZT3.2) strongly inhibit theexpression of the thiolase gene from the tac promoter. The location ofthese sequences can be narrowed down to the region between −84 (pZT3.5)and −124 (pZT3.4) as the deletion of this region results in the maximumlevel of tac-directed thiolase expression. Further deletions to −37(pZT3.5.1) and −26 (pZT3.5.2) do not increase the level of thiolaseexpression, and in fact a slight decrease is observed. It is importantto note that the time course of induction for this series of clonesfollows the same kinetics as pZT3 and is not appreciably affected by thedeletions.

In order to determine if the thiolase promoter lies in the region-84(pZT3.5) to −124 (pZT3.4), S1 nuclease protection experiments werecarried out according to the method of Berk and Sharp, Cell 12, 721-732(1977) on Z. ramigera RNA. Total RNA was isolated from a 100 ml mid-logphase culture by the hot phenol/glass beads extraction procedure ofHinnenbusch et al., J. Biol. Chem. 258, 5238-5247 (1983).5′-³²P-labelled DNA-probe was prepared as follows: 10 μg, plasmid pZT3.1DNA was digested to completion with Ava1 and subsequently treated withCIP; the Ava1 restriction fragments were labelled at the 5′-end with[gamma-³²P]-ATP and polynucleotide kinase; following EcoR1 digestion,the DNA was separated on an 8% acrylamide gel and the ³²P-labelled 280bp probe fragment eluted and recovered by ethanol precipitation. Probe(10,000 cpm) and 11 μg RNA were pooled, freeze dried, resuspended in 10μg hybridization buffer (40 mM pipes, pH 6.4; 1 mM EDTA, pH 8.0; 0.4 MNaCl; 80% (v/v) formamide), denatured for 10 min at 90° C. and annealedat 55° C. overnight. 235 microliters ice-cold S1 nuclease buffer (0.25 MNaCl; 30 mM NaOAc; 1 mM ZnSO₄; 200 μg single stranded calf thymus DNA)containing 2000 units of S1-nuclease was added followed by an incubationat 37° C. for 30 min. The reaction mixture was extracted once withphenol-chloroform and ethanol precipitated in the presence of 0.2 MNaOAc and 10 μg yeast tRNA carrier. The resulting fragments wereanalyzed on a 6% (w/v) acrylamide, 7 M urea DNA sequencing gel. For sizestandards, the Maxam Gilbert G and C sequencing reactions were performedon 50,000 cpm of 5′-³²P-labeled probe DNA. The results clearly show aprotected fragment and that the RNA start site is located at the C or Tresidue, position −86 or −87. A control indicates that in the absence ofZ. ramigera RNA, the probe is completely degraded, demonstrating thepresence of the thiolase promoter regions approximately 10 bp (−96) and35 bp (−121) upstream. The 5′-untranslated region of the thiolase is 86bp long.

From the results of the induction experiments, it is clear that thethiolase gene can be expressed at high levels in a soluble,catalytically active form in E. coli. S1-nuclease studies map thetranscription start site for the thiolase gene in Z. ramigera atnucleotides −86/−87.

Studies have demonstrated that although the “−35” region of the thiolasepromoter is recognized and binds the RNA polymerase, it is the “−10”region which determines the rate of transcription initiation. In thecase of pZT3, for example, the simultaneous binding of an RNA polymerasemolecule to both the bector and insert promoters would result in therapid initiation of transcription from the tac promoter which wouldsubsequently be impeded by the presence of the polymerase molecule boundat the Zoogloea promoter. The closer the two promoters are linked, theless chance of polymerase binding to both at the same time and the lowerthe inhibition. Therefore, this represents one means for controllingrate of expression of the enzyme.

Identification of the Z. ramigera Reductase gene.

After identifying the promoter region of the thiolase gene and notingthe absence of any potential terminator sequences downstream from thethiolase TAG stop codon, the remaining 2 kb of Zoogloea DNA present inclone pUCDBK1 was sequenced and examined for the reductase gene. Aseries of expression plasmids (pZT1-pZT3) containing either the entirepUDCBK1 insert or fragments thereof were constructed in the E. coli tacpromoter vector pKK223.3. Each plasmid has the thiolase gene located inthe correct orientation for expression from the tac promoter. It isreasonable to expect the tac promoter to direct not only thiolaseexpression but the expression of any genes located in the 2.3 kbdownstream in an operon-like type organization. Clone pZT1 wasconstructed by inserting the entire 3.8 kb EcoR1 Z. ramigera DNA insertfrom pUCDBK1 into the EcoR1 site of the vector pKK223-3. Subsequently,pZT2 was derived from pZT1 in a straightforward manner by deleting the850 bp Sma1 fragment. pZT3 is constructed as described for theidentification of the thiolase promoter. A series of tac promoterinduction experiments were performed on each of the recombinant clonespZT1, pZT2 and pZT3. The vector pKK223-3 was used as a control.

E. coli cells containing each of the plasmids were grown and induced bythe addition of isopropyl-beta-D-galactopyranoside (IPTG) to a finalconcentration of 2 mM. After 15 h induction, 10 ml cultures wereharvested and lysed by sonication. The cell lysates from each clone werethen analyzed both by enzyme assay and on SDS-PAGE. No PHB polymeraseactivity was detected in any of these lysates. Each of the threerecombinant plasmids pZT1, pZT2 and pZT3 demonstrate substantial levelsof thiolase activity. In addition, the lysates from pZT1 and pZT2 havecomparably high levels of AcAc-CoA reductase activity using NADPH as thecofactor. No reductase activity is detected in any of the lysates whenNADH is used as a cofactor. The control, pKX223-3, has neither thiolasenor reductase activities. To confirm that the lysates from pZT1 and pZT2do in fact contain the correct reductase, these lysates were alsoassayed for oxidation of D(−)beta-hydroxybutyryl-CoA. In both cases,enzyme activity was observed with NADP as electron acceptor.

Each of the lysates described above was also analyzed by SDS-PAGE. Theresults show the presence of the thiolase protein at around 42,000daltons in protein lysates from pZT1, pZT2 and pZT3, which is notpresent in the control, pKK223-3. Lysates of pZT1 and pZT2 also have asmall, 25,000 dalton protein which is not present in the lysate of pZT3or the control, which corresponds to the AcAc-CoA reductase. The resultsdemonstrate that the AcAc-CoA reductase gene is located downstream fromthe thiolase gene. The entire structural gene for this enzyme must belocated between the 3′-end of the thiolase and the first Sma1 sitedownstream in pUCDBK1.

Identification of the Translation Start Site and Overexpression of theReductase Gene.

The complete nucleotide sequence of the 2339 bp located 2.3 kbdownstream from the first Sal1 site in pUCDBK1 is shown in FIG. 2.Computer analysis of the sequence data, using codon usage informationfrom the thiolase gene as a standard, identified three open readingframes. N-terminal protein sequence data was obtained from the 25,000dalton band present in induced lysates from pZT1 and pZT2 followingpreparative SDS-PAGE and electroelution. This data was used to confirmthe translation start site for the corresponding gene. The N-terminalfive amino acids determined experimentally match residues 2 through 6predicted from the DNA sequence of the first open reading frame.Translation of this reading frame predicts a polypeptide of 25,000molecular weight. The translation product of the first open readingframe starting at the ATG, nucleotide 37 and ending at the TGA stopcodon nucleotide is shown in FIG. 2. This is the predicted primary aminoacid sequence of the acetoacetyl-CoA reductase protein.

It is evident that the acetoacetyl-CoA reductase gene in clones pZT1 andpZT2 can be expressed at reasonably high levels in E. coli. However, inboth of these cases, the expression of the reductase gene from the tacpromoter is not optimum due to the presence of the thiolase structuralgene and 5′-flanking sequence. A simpler acetoacetyl-CoA reductaseoverproduction vector, pZR14, was constructed. pUCDBK1 DNA was digestedto completion with Sal1 and Sma1 and the Sal1 ends repaired using theKlenow fragment of DNA polymerase. Following the addition of EcoR1linkers and digestion with EcoR1, the fragments were separated byagarose gel electrophoresis. The 1.05 kb fragment corresponding to theacetoacetyl-CoA reductase structural gene plus 36 bp flanking the 5′-endand 266 bp flanking the 3′ end was purified and ligated into the EcoR1site of pKK223-3. pZR14 was then identified as having the correctrestriction map with the reductase gene in the right orientation.Induction experiments were performed on pZR14 as described for pZT1,pZT2 and pZT3. Acetoacetyl-CoA reductase was expressed.

Identification of the Thiolase and Reductase Genes in A. eutrophus.

The methods used in isolating the first two PHB genes from Zoogloea wereapplied to the identification, isolation and characterization of genefrom another PHB producing species, Alcaligenes eutrophus, using theZoogloea thiolase gene region as a hybridization probe to locatehomologous sequences.

Subsequent sequence analysis of a 2 kb Pst1 fragment of A. eutrophus DNAcloned into pUC8 (clone pAeT3) identified the corresponding thiolasegene region in the A. eutrophus H16 genome. The downstream sequences inpAeT3 are also homologous to the NADP-linked reductase gene region fromthe Zoogloea clone pUCDBK1. The sequences of the Alcaligenes thiolaseand reductase genes is shown in FIG. 3.

Cloning of the individual thiolase and reductase genes from pAeT3 intopKK 223.3, leads to expression of the corresponding enzymes. Comparisonsof the Zoogloea and A. eutrophus thiolase protein sequences establishthat the two proteins are 63% homologous, including the active siteCys-89.

Both the A. eutrophus and Zoogloea thiolase gene regions were used ashybridization probes to screen Nocardia and Psuedomonas olevarans DNAfor homologous genes. Techniques for identifying the thiolase,reductase, and other synthetase genes from other species havinghomologous sequences in addition to those described above, are known tothose skilled in the art.

Identification of the Z. ramigera PHB Polymerase Gene.

PHB polymerase from Z. ramigera utilizes D(−)-hydroxybutyryl-CoAmonomers, polymerizing them in oxoester linkages in atemplate-independent head to tail condensation to yield linear polymers.These polymers can contain up to 10,000 monomer units with a molecularweight in excess of 1×10⁶. The polymer rapidly becomes insoluble andaccumulates as discrete granules in the cell.

As described in U.S. Ser. No. 067,695 filed Jun. 29, 1987, a conjugaltransfer system based on derivatives of the broad host range plasmidpRK290, described by Ditta et al., in Proc. Natl. Acad. Sci. USA 77,7347-7351 (1980), transposon mutagenesis and complementation analysiscan be used in conjunction with the isolation, characterization andcomplementation of PHB negative mutants to isolate the PHB polymerasegene for Z. ramigera and A. eutrophus. As described by Schlegel et al.,Arch. Microbiol. 71, 283-294 (1970), sudan-black staining is used forthe detection of PHB negative mutants. Complementation of the mutants isscreened for by growing, harvesting, and lysing the cells to release PHBthat can then be purified to determine its presence and molecular weightdistribution. Thiolase, reductase and PHB polymerase activities in thelysates are also assayed.

Identification of the A. eutrophus PHB Polymerase Gene.

These techniques were also applied to the cloning, sequencing andexpression of the PHB polymerase gene (phbC) in Alcaligenes eutrophusH16 using complementation of poly(β)-hydroxybutyrate-negative mutants ofA. eutrophus H16. The results demonstrate that the genes encoding thethree enzymes of the PHB biosynthetic pathway are organizedphbC-phbA-phbB. Expression of all three genes in E. coli results in asignificant level (50% dry cell weight) of PHB production in thisbacteria. phbC encodes a polypeptide of Mr=63,900 which has a hydropathyprofile distinct from typical membrane proteins indicating that PHBbiosynthesis probably does not involve a membrane complex.

The strategy of constructing, characterizing and complementingPHB-negative mutants of a derivative (11599 S1, Table 1) of A. eutrophusH16 was used to identify and isolate the gene(s) encoding PHBpolymerase. Transposon mutagenesis allowed use of DNA hybridizationanalysis to map the chromosomal location of the Tn5 insertion in anyinteresting strains. 32 potential PHB negative mutants were identifiedby their opaque colony phenotype when grown on nitrogen limited minimalagar plates. Due to the procedure used to enrich for PHB-deficientstrains, it was not surprising that the 32 mutants were found by DNAhybridization using a Tn5 DNA probe to belong to only three classes.More detailed DNA hybridization studies were then used to analyze arepresentative from each class, i.e., strains PHB #2, PHB #3 and PHB#19. From these studies, it was possible to conclude that in the case ofstrain PHB #2 and strain PHB #3, the Tn5 insertion causing the opaquephenotype was located in the chromosome approximately 1.2 kb and 1.6 kb,respectively, upstream from the phbA-phbB genes, as illustrated on FIG.3. For strain PHB #19, the Tn5 insertion was located elsewhere on the A.eutrophus chromosome.

The experimental procedure and materials used in the isolation andcharacterization of phbC were as follows. The procedures and materialsare similar to those described for isolation of the phbA and phbB genes.

Bacterial strains and plasmids are shown in Table 1. Media and cultureconditions are as decribed above. TABLE 1 Bacterial Strains andPlasmids. Relevant Characteristics Reference Strain E. coli JM83 DH5αHost strain for plasmids BRL A. eutrophus H16 Wild type strain ATCC1769911599 — NCIB 11599 11599S1 Strep^(r) PHB#2 H16[phb2::Tn5] PHB#3H16[phb3::Tn5] PHB#19 H16[phb19::Tn5] Plasmids pAeT29 phbA-phbB pAeT10phbA-phbB pLAFR3 Tc^(r), cosmid vector B. Staskawicz pRK2013 Nm^(r)pRK602 Cm^(r), Nm^(r), pRK2013 nm::Tn9 containing Tn5 pUC18 Ap^(r) pUC19Ap^(r)

DNA manipulations were similar to those described above. Restrictionendonucleases, T4 DNA ligase and DNA polymerase 1 were obtained from NewEngland Biolabs and used as directed by the manufacturer. Calfintestinal alkaline phosphatase was purchased from Boehringer MannheimCorporation. All routine DNA manipulations, including plasmidpurifications, E. coli transformations, etc. were performed usingmethods described by Maniatis, et al. Chromosomal DNA was purified fromA. eutrophus strains, grown to late logarithmic phase in TSB asdescribed previously. Transfer of restriction digested DNA samples fromagarose gels to nitrocellulose filters, prehybridization andhybridization with ³²P-labelled DNA probes was as previously described.Rapid plasmid isolation from A. eutrophus recombinant strains, forrestriction analysis, was performed by the alkaline extractionprocedure.

Conjugation in A. eutrophus.

The conjugal transfer of the broad host range plasmid, pLAFR3, orrecombinant derivatives of pLAFR3, into A. eutrophus was performed usingthe same method as previously described. In this case, however, therecipient A. eutrophus cells were not sonicated and transconjugants wereselected on A. eutrophus mineral agar plates containing 0.01% NH₄Cl asnitrogen source, 1% (w/v) fructose as carbon source and 10 μg/mltetracycline.

For Tn5 mutagenesis, a spontaneous streptomycin resistant strain of A.eutrophus 11599 (1599 S1) was used. Transfer of pRK602 (Tn5) was carriedout as described above using E. coli MM294A (pRK602) as the only donor.A. eutrophus strains containing Tn5 were selected for by growth onstreptomycin (500 μg/ml) and kanamycin (100 μg/ml).

Amplification and Identification of PHB-Deficient Mutants.

The amplification and screening procedures described by Schlegel andOeding, Radiation and Radioisotopes for Industrial Microorganisms.International Atomic Energy Agency, Vienna, 223-231 (1971) was used toidentify PHB-deficient strains of A. eutrophus. A pool of around 10⁵Kan^(r) transconjugants (Tn5 insertion mutants) was inoculated into 10ml of mineral media containing 0.01% NH₄Cl, 1% fructose and 100 μg/mlkanamycin and incubated for 18 h at 30° C. This culture was then used toinoculate 100 ml of the same medium and incubated for 30 h at 30° C. Toamplify PHB-deficient mutants, aliquots of this culture containingapproximately 10⁹ cells were fractionated on sucrose step gradients bydensity equilibrium centrifugation and plated out on mineral agar platescontaining 0.01% NH₄Cl, 1% fructose and 100 μg/ml kanamycin. Aftergrowth for 4-5 days at 30° C., opaque (PHB-deficient) and white(PHB-containing) colonies were readily distinguished. By quantitatingthe level of PHB produced by both opaque and white colonies, it wasconfirmed that opaque colonies were PHB-deficient whereas white coloniescontained PHB.

Analysis of Proteins.

In order to perform assays for β-ketothiolase, NADPH-linkedacetoacetyl-CoA reductase and PHB-polymerase, 100 ml cultures of A.eutrophus strains were grown at 30° C. for 40 hours in TSB. For Tn5mutant strains, kanamycin was added at 100 μg/ml and for strainscontaining pLAFR3 or derivatives thereof, tetracycline was added to 10μg/ml. Cells were harvested by centrifugation, resuspended in 2 ml lysisbuffer (10 mM Tris HCl, pH 8.0; 5 mM β-mercaptoethanol; 5 mM EDTA, 0.02mM phenyl-methyl-sulfonyl-fluoride; 10% v/v glycerol) and lysed bysonication. An aliquot of the lysate was cleared of cell debris bycentrifugation for β-ketothiolase and acetoacetyl-CoA reductase assays.β-ketothiolase activity was determined by measuring the rate ofthiolysis of acetoacetyl-CoA as described by Davis, et al., J. Biol.Chem. 262, 82-89 (1987), of acetoacetyl-CoA with NADPH as the cofactor.PHB polymerase assays were performed using samples of the crude lysateand determining the level of incorporation of D-³H-hydroxybutyryl-CoA(specific activity approximately 2 μCi/μmol), as described by Fukui, etal., Arch. Microbiol. 110, 149-156 (1976). Protein concentrations weredetermined by the method of Bradford, Anal. Biochem. 72, 248-254 (1976),using Biorad assay solution and bovine serum albumin as the standard. E.coli maxi-cell labelling studies were performed as described by Sancar,et al., J. Bacteriol. 137, 692-693 (1979).

PHB Purification and Quantitation.

To determine the level of PHB in different strains, 100 μl aliquots ofthe crude lysates were treated with 1.2 ml of 5% Na hypochloritesolution for 1 h at 37° C. The insoluble PHB was then harvested bycentrifugation for 10 min in a microcentrifuge, washed successively with1 ml of H₂O, 1 ml acetone, 1 ml of ethanol and dried under vacuum. PHBconcentrations were then determined spectrophotometrically as describedby Law and Slepecky, J. Bacteriol. 82, 33-36 (1961) using a standardcurve and expressed as mg PHB/mg protein.

Plasmid Constructions and Complementation Analysis.

Plasmids pLA29, pLA40, pLA41 and pLA42 were constructed by cloningrestriction fragments of the pAeT29 insert into the broad host rangevector pLAFR3 for complementation analysis of the PHB-negative A.eutrophus strains. pLAFR3 is a derivative of pLAFR1, described byFriedman, et al., Gene 18, 289-296 (1982), containing a pUC8 polylinkercloning site inserted into the EcoR1 site. Different fragments of pAeT9were cloned into pLAFR3. pLA29 was constructed by ligating the entire 15kb EcoR1 insert from pAeT29 into the EcoR1 site of pLAFR3. To facilitatethe construction of pLA40, pLA41 and pLA42, the corresponding fragmentswere first cloned into pUC18 to produce plasmids pAeT40, pAeT41 andpAeT42. The fragments were then excised by digestion with BamHI andEcoR1 from the pUC18 plasmids, purified following agarose gelelectrophoresis and ligated into BamH1/HindIII digested pLAFR3. Toconstruct pAeT40, pAeT29 DNA was digested to completion with Nde1 andthe cohesive ends filled in using the Klenow fragment of DNA polymerase.After separating the fragments on an agarose gel, the 7 kb fragment ofinterest was purified by electroelution, ligated into the Sma1 site ofpUC18 and the recombinant plasmid pAeT40 subsequently identified byrestriction analysis after transforming E. coli DH5a cells. Thisconstruction eliminates the acetoacetyl-CoA reductase activity since oneof the Nde1 sites is located within the structural gene for this enzyme.For the construction of pAeT41, Sma1/EcoR1 digested pAeT29 DNA wasseparated on an agarose gel and the 5 kb Sma1/EcoR1 fragment purifiedand ligated into Sma1/EcoR1 digested pUC18 to give the correct plasmid.Deletion of the 2.3 kb Pst1 fragment containing the β-ketothiolase andacetoacetyl-CoA reductase structural genes by partial Pst1 digestion ofpAeT41 DNA and religation was used to construct pAeT42.

Hybridization Mapping of Tn5 Insertions.

A library of 10⁵ individual Tn5 insertion mutants of A. eutrophus 11599S1 was constructed and 32 potentially PHB-negative colonies, identifiedby their opaque colony phenotype on nitrogen limited minimal plates, asdescribed above. These were further characterized using Southern DNAhybridization analysis. For the DNA hybridization studies restrictiondigested chromosomal DNA from each strain was analyzed using both a Tn5DNA probe (plasmid pRK602) and two plasmids, pAeT10 and pAeT29 whichcontain the A. eutrophus phbA-phbB locus (FIG. 3).

The 32 “opaque” strains represented multiple copies of only threedistinct mutant types. These three distinct mutant types are representedby strains PHB #2, PHB #3 and PHB #19. For strains PHB #2 and PHB #3,the transposon Tn5 is inserted into chromosomal Pst1 fragments of 2.3 kband 0.6 kb, respectively. Both of these chromosomal Pst1 fragments arelocated on the 15 kb of A. eutrophus DNA cloned in plasmid pAeT29, butnot in the phbA-phbB structural genes. Strain PHB #19 has Tn5 insertedinto a Pst1 fragment, not present on the pAeT29 plasmid.

More detailed DNA hybridization experiments were performed on thechromosomal DNA from strain PHB #2 and strain PHB #3 to map the site ofthe Tn5 insertion in each of these mutants. Chromosomal DNA from each ofthese strains as well as the wild type strain H16 and strain PHB #19 wasdigested with Sal1, Sma1 and BglII, transferred bidirectionally tonitrocellulose filters and hybridized with Tn5 DNA (pRK602) and pAeT29DNA probes to map the location of the Tn5 insertions in strains PHB #2and PHB #3.

The results of a biochemical analysis of wild type H16 and each of themutuant strains PHB #2, PHB #3, and PHB 019 is presented in Table 2. 100ml stationary phase cultures of each strain were harvested, lysed andassayed for PHB content and β-ketothiolase, NADP-specificacetoacetyl-CoA reductase and PHB polymerase activities. Under thesegrowth conditions wild type H16 produces a significant level of PHB (1.3mg PHB/mg protein, Table 2) and has a high level of all three enzymeactivities. Mutant strains PHB #2 and PHB #3 produce essentially no PHBand strain PHB #19 produces only 5% of the wild type level (Table 2).PHB polymerase activity could not be detected in any of these mutantstrains, however, the presence of PHB in the lysate of strain PHB #19indicates that the enzyme is there although the activity is probablybelow the detection level of the assay. β-ketothiolase activities in allthree mutants are reduced to the order of 45% (PHB #2) to 38% (PHB #19)that of wild type strain H16. Similarly, NADP-specific acetoacetyl-CoAreductase activities are around 50% of the wild type level. It wasconcluded from these data that the PHB-polymerase gene was locatedupstream from phbA-phbB and that the expression of the later genes isaffected by the Tn5 insertion upstream in the case of strains PHB #2 andPHB #3.

A series of plasmids containing fragments of the A. eutrophus insert ofplasmid pAeT29 were constructed in the broad host range vector pLAFR3for complementation analysis of the PHB-negative mutants.

Each of the recombinant plasmids, pLA29, pLA40, pLA41 and pLA42 wereintroduced into each of the A. eutrophus strains by conjugation and theresulting transconjugants analyzed on nitrogen limited plates for therestoration of the white (PHB plus) phenotype. Plasmids pLA29, pLA40,pLA41 and pLA42, each of which contains the region upstream fromphbA-phbB into which Tn5 has inserted in the chromosome of strains PHB#2 and PHB #3, complemented the mutation in each of these two strains,restoring the white colony phenotype. All four recombinant plasmids alsorestored the wild type colony phenotype to mutant strain PHB #19. In thecase of this strain, the Tn5 insertion is located outside the region ofthe A. eutrophus chromosome contained in each of the plasmids. Controlexperiments using the vector pLAFR3 resulted in the opaque colonyphenotype when introduced into each of the three mutant strains.

Biochemical analysis of each of the complemented strains was performedas described for the characterization of the mutants and these resultsare also presented in Table 2. The introduction of pLA29 into each ofthe mutant strains results in the restoration of PHB polymerase activityand PHB biosynthesis (Table 2). In addition, an approximately three tofive-fold increase in the levels of β-ketothiolase and NADP-specificacetoacetyl-CoA reductase activities was observed. Plasmid pLA40 andpLA41 also restore PHB-polymerase and PHB production to strains PHB #2(Table 2), PHB #3 and PHB #19, although in the case of pLA40, the phbBgene was disrupted during the construction of this plasmid. Finally,plasmid pLA42 restores PHB polymerase activity and PHB production to allthree mutant strains although the phbA-phbB genes have been deleted. Inthe case of strains containing this plasmid the β-ketothiolase andNADP-specific acetoacetyl-CoA reductase activities remain at the samelevel as the mutant strains (Table 2). TABLE 2 Biochemical analysis ofmutant and complemented A. eutrophus H16 strains. Polymerase³ StrainPHB¹ Thiolase² Reductase² (×10³) H16 1.3 8.9 1.0 3.9 PHB#2 <0.01 4.0 0.5ND PHB#3 <0.01 3.4 0.5 ND Tn5#19 0.6 3.2 0.4 ND H16/pLA29 1.0 28.7 9.25.3 PHB#2/pLA29 1.5 27.5 3.5 3.8 PHB#3/pLA29 0.9 24.8 4.4 0.7PHB#19/pLA29 1.8 26.7 4.9 1.0 PHB#2/pLA40 0.9 20.4 0.45 0.6 PHB#2/pLA4118.0 3.7 0.9 PHB#2/pLA42 1.2 2.0 0.3 4.3 PHB#3/pLA42 0.9 5.5 0.5 0.6PHB#19/pLA42 1.2 5.5 0.4 0.6¹mg/mg of protein²units/mg of protein³cpm/min/mg of proteinND: no detectable activityResults shown are the average of two or more experiments.

As described above, the phbA-phbB genes located on plasmid pAeT29 wereexpressed in E. coli under the control of the A. eutrophus promoter.Identification of the phbC gene upstream from phbA-phbB together withthe observed decrease in thiolase and reductase enzyme activities instrains PHB #2 and PHB #3 indicates that all three genes are expressedfrom a single promoter located upstream from phbC. To study this,cultures of E. coli strains containing plasmids pAeT41 and pAeT42 weregrown under nitrogen limiting conditions until cells reached stationaryphase at which point the cells were harvested, lysed and analyzed. E.coli containing pUC18 was used as a control. The results ofβ-ketothiolase, acetoacetyl-CoA reductase, PHB polymerase and PHBconcentration assays, shown in Table 3, indicate that the lysate of E.coli containing plasmid pAeT41 has a significant level of each enzymeactivity and PHB production.

Maxi-cell analysis of the E. coli strains described above was used todetermine the molecular weight of the polypeptides encoded by plasmidspAeT41 and pAeT42. Plasmid pAeT10 was included in the analysis as thisplasmid expresses the A. eutrophus phbA-phbB genes from the pUC8 vectorlacZ promoter. Additional protein bands are present of Mr 40,000 and Mr26,000 in lanes 1 and 2 containing plasmid pAeT10 and pAeT41,respectively. Both of these plasmids express the phbA-phbB genesencoding 3-ketothiolase (Mr 41,000) and NADP-specific acetoacetyl-CoAreductase (Mr 26,000). Neither of these two proteins is present in theextract of cells containing plasmid-pAeT42 (lane 3) which does notcontain the phbA-phbB genes. Control experiments in which the vectorpUC8 was used gave no signal at Mr 41,000 or Mr 26,000. Both plasmids,pAeT41 and pAeT42, express the PHB polymerase (phbC) gene in E. coli,and in lanes 2 and 3 which contain extracts of cells containing theseplasmids a signal at Mr 58,000 is clearly evident. Again, this proteinis absent from lane 1 which contains the extract from cells containingplasmid pAeT10 which does not contain the phbC gene and also from acontrol sample of pUC8 containing cells. An additional band of around Mr30,000 is present in all 3 lanes and was also found in controlexperiments of cell extracts containing pUC8 and is presumably a vectorprotein. From these data we conclude that the phbC gene expressed in E.coli encodes a polypeptide of approximately M_(r) 58,000. TABLE 3Biochemical analysis of recombinant E. coli strains to determineexpression of phbC-A-B in E. coli. Thiolase Reductase Polymerase PHBU/mg U/mg cpm/min/mg mg/mg Plasmid Protein Protein Protein Protein pUC180.5 ND ND 0.015 pAeT41 59.0 2.5  2.4 × 10⁴ 2.977 pAeT42 0.9 ND 0.02 ×10⁴ 0.011ND: no detectable activityResults shown are the average of two or more experiments.

Nucleotide Sequence Analysis of phbC.

The 2 kb Sma1-Pst1 A. eutrophus chromosomal DNA fragment cloned inplasmid pAeT42 contains the entire structural gene for phbC and probablythe regulatory sequences. This fragment was sequenced from both DNAstrands multiple times using the dideoxy sequencing method as describedabove. A single long open reading frame extends from nucleotide 820 to aTGA stop codon at nucleotide 2608. Potential translation initiationcodons are present at position 842 (ATG), 1067 (ATG) and 1097 (ATG).Translation from each of these potential start sites would produceproteins of Mr 63,940, Mr 55,513 and Mr 54,483, respectively.Significant amino acid sequence homology between the translation productfrom the ATG at position 842 to the ATG at position 1067 and the P.oleovarans PHA polymerase gene product, described below, indicates thatthe first ATG (position 842) is probably correct. FIG. 4 presents theentire nucleotide sequence of this region from the Sma1 site to thefirst 30 nucleotides of the phbA gene located downstream. Thetranslation product of the open reading frame from the ATG at position842 to the TGA at position 2609 is also shown. The PHB polymeraseencoded by the phbC gene in plasmid pAeT42 is a polypeptide of 589 aminoacids with an Mr=63,940. The N-terminal 10 amino acids of the phbA geneproduct are also presented in FIG. 4. Additional features of thenucleotide sequence presented in FIG. 4 include the C-terminus of anopen reading frame which begins upstream from the Sma1 site andterminates at the TGA stop codon at position 76. Located 85 bpdownstream from the phbC TGA stop codon (position 2609) lies the ATGstart codon for the phbA structural gene (position 2969). From thesedata it is clear that the three enzymes of the A. eutrophus PHBbiosynthetic pathway are encoded by three genes organized asphbC-phbA-phbB as illustrated in FIG. 4.

The expression of phbC alone in E. coli produces neither PHB norsignificant levels of PHB polymerase activity (plasmid pAeT42). E. coliappears incapable of synthesizing D-(−)-hydroxybutyryl-CoA, as substratefor PHB polymerase, in the absence of the A. eutrophus phbA-phbB genes.Since the insert of pAeT42 contains both the promoter and structuralgene for phbC (plasmid pLA42 complements all PHB-negative mutants, Table2), it can be concluded that in the absence of available substrate, PHBpolymerase is inactive or degraded in E. coli.

The nucleotide sequence of the A. eutrophus chromosomal DNA insert inplasmid pLA42 encoding PHB polymerase predicts a single polypeptide ofMr 63,940 (FIG. 4). Although PHB polymerase has not previously beenpurified and characterized, the results of E. coli maxi-cell studiesindicate a Mr=58,000 for this polypeptide, in reasonable agreement withthat predicted from the gene sequence.

For a number of years, it was proposed that the polymerization of(D)-β-hydroxybutyryl-CoA involves a membrane bound polymerase whichforms a type of barrier between the aqueous environment of the cytoplasmand the hydrophobic crystalline PHB granules. The hydropathy profile ofthe PHB polymerase polypeptide does not indicate a typical membranespanning structure. In addition, NMR studies of native PHB granules inMethylobacterius indicate that these granules are in a mobile, asopposed to a highly crystalline solid state. Together these data lendcredence to the idea that PHB biosynthesis does not in fact require acomplex membrane bound polymerization system. The mechanism for PHBpolymerase proposed in the literature involves two partial reactions.The initial acyl-S-enzyme intermediate formation is followed by transferto a primer acceptor in the second reaction. The predicted primarystructure of PHB polymerase has 5 cysteine residues, Cys₂₄₆, Cys₃₁₉,Cys₃₈₂, Cys₄₃₈ and Cys₄₅₉.

Identification of the P. oleovarans PHA Polymerase Gene.

The genes involved in the biosynthesis of polyhydroxyalkanoate (PHA)polyesters in Pseudomonas oleovarans were also isolated, as follows.

In 1983, de Smet, et al. J. Bacteriol. 154, 870-878, identified apolymer produced by Pseudomonas oleovarans TF4-1L (ATCC 29347) aspoly-B-hydroxyoctanoate. Subsequent studies showed that P. oleovaranscould produce a range of PHA biopolymers depending on the carbon sourceused, i.e., n-alkanes and 1-alkenes (Lageveen, et al, Appl. Environ.Microbiol. 54, 2924-2932 (1988)) or fatty acids (Brandl, et al., App.Environ. Microbiol. 54, 1977-1982 (1988). The pathway appears to involvethe conversion of the alkanes/alkenes to the fatty acid which thenenters the fatty acid B-oxidation pathway, resulting in the formation ofthe D isomer of the B-hydroxyacyl-CoA, which is incorporated into thepolymer by PHA polymerase. P. oleovarans has not been shown toincorporate B-hydroxybutyrate indicating that 1) it does not possess thethiolase/reductase enzymes, or 2) the PHA polymerase cannot useB-hydroxybutyrate as a substrate. The broad range of substrates used bythe P. oleovarans PHA polymerase make the gene encoding this enzymeparticularly interesting for biopolymer engineering of polyesters.

The approach used for isolating the A. eutrophus B-ketothiolase andNADP-specific acetoacetyl-CoA reductase using the Z. ramigeraB-ketothiolase gene as a DNA hybridization probe was followed, asdescribed above, to isolate the P. oleovarans PHA polymerase gene.Southern DNA hybridization of P. oleovarans chromosomal DNA identified a6 kb EcoR1 restriction fragment with strong homology to the A. eutrophusPHB polymerase gene (phbC). The 6 kb EcoR1 fragment was cloned in the E.coli plasmid vector, pUC18, by standard procedures to give plasmidpP023. The region which hybridized to the A. eutrophus phbC gene islocated as indicated on FIG. 5. Nucleotide sequence analysis of thecomplete 6 kb fragment identified three potential protein coding regions(open reading frames, ORF1, ORF2 and ORF3, indicated on FIG. 5). ORF1begins at the ATG initiation codon nucleotide 554 and ends at the TGAstop codon nucleotide 2231 (FIG. 6). This open reading frame iscontained in the region of the pP023 insert which hybridizes with the A.eutrophus phbC gene. ORF1 encodes a polypeptide of 562 amino acids withan Mr=60,000. A comparison of the protein sequence predicted bytranslation of ORF1 with the amino acid sequence of the A. eutrophus PHBpolymerase using the program ALIGN revealed 52% identity between the twoproteins. These data identify ORF1 as the P. oleovarans PHA polymerasegene. ORF3 begins at the ATG position 2297 and ends at the TAA position3146. ORF2 begins at the ATG position 3217 and ends at the TGA position4948. ORF2 and ORF3 are probably co-transcribed with the PHA polymerasegene (ORF1) and are probably proteins involved in PHA biosynthesis.

Synthesis of PHB, PRA and Similar Polymers.

It was established above that it is possible to construct new PHBproduction strains by introducing the A. eutrophus PHB biosyntheticgenes into E. coli resulting in the accumulation of up to 50% dry cellweight as PHB. The construction of new or improved polyester productionstrains is now possible by the expression of either the PHB biosyntheticgenes from A. eutrophus or the PHA polymerase gene and ORF2 and ORF3from P. oleovarans in a number of systems. Plasmids can be constructedwhich express the A. eutrophus B-ketothiolase and NADP-specificacetoacetyl-CoA reductase genes in P. oleovarans under the control ofthe xylS promoter in the broad host range expression plasmids pNM185(Mermod, et al., J. Bacteriol. 167, 447-454 (1986), or pERD20/pERD21(Ramos, et al, FEBS LETTERS 226, 241-246 (1986). Alternatively, thebroad host range tac promoter expression vectors pMHB24/pMMB22(Bagdasarian, et al, Gene 26, 273-282 (1983)). These same vectors canalso be used to express the A. eutrophus PHB polymerase gene or thethree P. oleovarans genes cloned in plasmid pP023 (FIG. 5).

Two plasmids, pLAP1 and pLAP2, have been constructed which shouldexpress the P. oleovarans PHA polymerase gene and ORF2 (pLAP1) or thePHA polymerase gene and ORF2 plus ORF3 (pLAP2) under the control of theA. eutrophus phbC promoter (FIG. 4).

To construct these plasmids, the 810 bp Sma 1-BstB 1 restrictionfragment spanning the first 810 nucleotides of the A. eutrophus insertin plasmid pAeT42 containing the phbC promoter was ligated into theunique Sma 1 site in the E. coli vector pUC19 to obtain plasmid pAeTB1.The P. oleovarans PHA polymerase gene promoter was removed by using theexonuclease Bal31 to delete 170 bp from the end of Fsp1 digested pPO23DNA and recovering the PHA polymerase structural gene plus ORF2 bysubsequently digesting with Cla1, and cloning the fragment intoSma1/Cla1 digested pBLSK+ vector (Stratagene, La Jolla Calif. 92037).The insert of pPOB10 was identified as containing the last 19 bpupstream from the ATG start codon of the PHA polymerase structural gene(nucleotide 535, FIG. 6) the complete PHA polymerase structural gene andORF2. The structural gene and ORF2 could then be recovered on a 2.6 kbBamH1-Xho1 fragment and ligated into BamH1/Sal1 digested pAeTB1 toobtain plasmid pAeP1. The entire insert of pAeP1 containing the phbCpromoter—PHA polymerase structural gene—ORF2 construct was then excisedas a 3.4 EcoR1-HindIII fragment and cloned into the polylinker region ofthe broad host range vector pLAFR3 for conjugation into A. eutrophusstrains. To construct pAeP2, the 2.6 kb BamH1-Cla1 fragment from pPOB10and the 2.5 kb Cla1-Xho1 fragment from pP023, containing ORF3, wereligated with BamH1/Sal1 digested pAeTB1 to obtain pAeP2. Again thephbC-PHA polymerase-ORF2-ORF3 construct could be excised as a 5.9 kbEcoR1-HindIII fragment and cloned into the polylinker region of pLAFR3to obtain pLAP2. pLAP1 should express both the PHA polymerase and ORF2in A. eutrophus and pLAP2 should in addition express ORF3. If the genesare not expressed, they can be inserted into the broad host rangeexpression vectors described above for the B-ketothiolase andNADP-specific acetoacetyl-CoA reductase genes.

The PHB polymerase and PHA polymerase genes should prove invaluable forthe production of PHA polymers in bacterial and plant systems. However,the cloned and characterized genes can be further modified byconstructing fusions of the two polymerases or by chemical mutagenesis.Functional polymerase enzymes could then be selected in an appropriateorganism by the accumulation of polymer detectable by phenotypicappearance or increased density. This is a straightforward approach toaltering the enzyme's specificity to create novel polymerases.

Notification of Polymer Synthesis by Varying Levels of EnzymeExpression.

After isolation and characterization of the polymer genes and geneproducts from a variety of organisms, as demonstrated for Z. ramigera,A. eutrophus, N. salmonicolor, and P. oleovarans, a means forcontrolling the expression of the gene products can be established.Overproduction of the Zoogloea thiolase gene was demonstrated by thestudies used to define the transcription start site and promoter of theZ. ramigera. Overproduction enables the purification of the enzymes tohomogeneity and provides reagent type quantities for analysis andcomparison of substrate specificieties. In addition, the purifiedenzymes can be used to synthesize stereospecific substrates for in vitropolymer synthesis. Further, once the transcriptional regulatorymechanism responsible for polymer overproduction is elucidated under avariety of environmental conditions, in vitro systems for the enzymaticsynthesis of known polymers, and novel polymers, can be developed toprovide new materials. The new materials are then analyzed for chemicalcomposition, molecular weight and Theological characteristics so thatmaximum utilization can be made of the polymers.

An overproduction system for the Z. ramigera thiolase in E. coli wasconstructed using the synthetic tac promoter to produce a series ofthiolase expression plasmids, the optimum construct in induced in E.coli cells yielding about 20-30% of the total soluble cell protein asthiolase. This method yields thiolase in reagent type quantities, anaverage of 150 mg of pure thiolase from 1 liter of culture.

There are essentially two conditions where gene regulation in Z.ramigera and A. eutrophus may be expected to occur: when carbon starvedcells under nutrient limiting conditions are subsequently presented witha carbon source and when cells grown under nutrient limiting conditionshave accumulated large amounts of PHB and the nutrient limitation isremoved, resulting in PHB degradation.

Transcriptional regulation of the polymer biosynthetic genes isdetermined as follows. Cultures grown under various conditions areharvested both for enzyme assays (thiolase, reductase and synthetase)and for RNA purification. RNA samples are analyzed in a series ofNorthern hybridization experiments using the cloned genes as probes.Useful RNA hybridization methodology includes glyoxylation of RNA(McMaster and Carmichael, Proc. Natl. Acad. Sci. USA 74, 4835 (1977));formaldehyde/agarose gel electrophoresis (Lehrach et al., Proc. Natl.Acad. Sci. USA 16, 4743 (1977)); transfer to nitrocellulose or nylonfilters (Thomas, Proc. Natl. Acad. Sci. USA 77, 5201 (1980)); andhybridization with DNA probes labelled with ³²P by nick translation(Rigby et al., J. Mol. Biol. 113, 237 (1977)). DNA probes are preparedfrom clones pUCDBK1 (Z. ramigera); and pAeT3 (A. eutrophus). One resultof these studies is the establishment of the operon organization of thegenes and the length of the mRNA.

The levels of each of the biosynthetic enzymes are manipulated and theeffect this has on polymer synthesis monitored. It is necessary todetermine the rate-limiting enzyme(s) in the biosynthetic pathway sothat one can increase flux through the pathway by overproducing therate-limiting enzyme(s); the effect overproduction of each enzyme has onthe incorporation of different monomeric units, i.e., the ratio ofPHB:PHV in the copolymer produced by A. eutrophus when grown onbutyrate; and the result of expression of the genes from one species inother species, for example, the expression of Zoogloea genes in A.eutrophus and vice versa, as well as other isolated and characterizedheterologous genes from other organisms, e.g., Nocardia and P.oleovarans in Zoogloea and A. eutrophus.

To accomplish overproduction of polymer biosynthetic genes in multiplehost organisms, one must use broad host range expression vectors whichfunction in these bacteria. In one instance, enzyme overproduction viagene dosage is carried out. For example, the entire pUCDBK1 insertcontaining the promoter region can be cloned into the vector pSUP104(Simon et al., Molecular Genetics of the Bacteria-Plant Interaction, A.Pobler, ed. (Spring-Verlag, NY 1983) and used to transform Z. ramigeraI-16-M. The extent of overproduction of each enzyme is monitored byenzyme assays. A similar approach can be taken for any number of othergenes; for example, thiolase;

-   -   thiolase and reductase; reductase; reductase and synthetase,        etc. Secondly, genes can be placed under the transcriptional        control of high efficiency promoters, i.e., tac (Gill et al., J.        Bact. 167, 611-615 (1986) and tol (Mermod et al., J. Bact. 167,        447-454 (1986). In this case, the constructs are conjugated into        mutants defective in the corresponding gene. The expression of        the polymer biosynthetic gene or genes of interest can then be        tightly regulated, as determined using enzyme assays to monitor        the level of overproduction. As each construct is tested, one        can begin to monitor the effect on polymer synthesis in a        routine manner i.e., the rate and level of synthesis.        Notification of Polymer Synthesis by Altering Available        Substrate or Enzyme Specificity.

Factors which determine the molecular weight of the PHB or PHA producedby different bacteria can be eludicated by analysing the molecularweight distribution of the polymers produced by various bacteria. Thereis little doubt that a number of PHB-producing microorganisms have theability to incorporate monomers other than D(−)-hydroxybutyrate into thepolymer chain. For the PHB-PHV copolymer produced by A. eutrophus, ithas been proposed that propionate is first converted to propionyl-CoAwhich then acts as a substrate for beta-ketothiolase. The high yields ofpure enzymes available from overproduction systems is necessary todetermine the range of alternate substrates which each of the threePHB-biosynthetic enzymes can utilize and the types of new PHB-likepolymers that can be synthesized in an in vitro system where theavailable substrates can be strictly controlled.

Although the thiolase and reductase enzymes are an essential part of thebiosynthesis of PHB and PHB-like polymers, it is the PHB polymerasewhich ultimately defines the new types of polymer which can be made.This is facilitated by the development of an in vitro system using theenzyme to test a whole range of substrates, many of which cannot enterthe cell and therefore cannot be tested for incorporation into PHB by afermentation process.

Overproduction and purification of more than one reductase enzymeprovides a means for comparing the kinetics and specificity of theenzymes. The Zoogloea reductase has been reported to be NADP-specific,however, the A. eutrophus enzyme apparently will use either NAD or NADP.The stereospecificity of this enzyme may make it a useful reagent forthe synthesis of D-substrates for PHB polymerase studies. Among theacetoacetyl derivatives to be tested are the oxoester of CoA andoxopantetheine pivaloate (OPP) and the methylene analogs. The ketone butnot the oxoester of the methylene analogs is cleaved by Zoologeathiolase.

Various longer chain alkyl derivatives where R does not equal H, and inparticular the C₅-C₈ linear 3-oxo thiolesters, oxoesters and methyleneketones, may also be useful as substrates for the PHB polymerase, giventhe existence of C₃-C₉-beta-hydroxyalkanoates in B. megaterium, as wellas olefins, alcohols and epoxides.

In crude extracts of Z. ramigera, D-beta-hydroxybutyryl CoA, but notL-hydroxybutyryl CoA, is a substrate for PHB polymerase. It is expectedthat other D-hydroxyacyl CoA species can utilize alternate substrates orcosubstrates such as D-beta-hydroxyvaleryl CoA (HV-CoA). [2-³H]HB-CoAand beta[3-¹⁴C]-HV-CoA, each readily preparable by enzymic or chemicalsynthesis, can be used as substrates and to monitor ³H and ¹⁶C contentand ratios in polymers precipitated or separated by gel filtration. Itis predicted that block copolymer regions, e.g., (HB)₅₀₀ (HV)₁₀₀₀(HB)₅₀₀ can be constructed by careful control of substrate ratios, andleaving groups in elongation phase, e.g., HB-oxo-CoA and HV-S-CoAmonomers.

Additional alternate substrates can be tested including branched chainbeta-hydroxyacyl CoAs. Testing cannot be done in whole cells since suchcompounds are not normally transported into the cells. Alternatesubstrates can be tested for inhibition of normal [¹⁴C]-PHB formationfirst by incorporation of soluble [¹⁴C]-HBCoA into insoluble polymer,then as copolymerization cosubstrates and finally forhomopolymerization. Alternate substrates can be assayed for K_(m),V_(max) relative to HB-CoA and for polymer size determined by calibratedgel filtration studies.

Method for Production of PEB on a Continuous Basis.

PHB is produced and stored in bacteria when they are grown undernutrient limiting conditions, usually nitrogen-limiting conditions (forexample, 0.1% nitrogen, depending on the species), although culturingthe bacteria under conditions providing limited oxygen, phosphate, orother non-carbon nutrient source will also induce PHB synthesis andstorage. For example, Azotobacter beijerinckii, a nitrogen fixingbacteria accumulates up to 70% dry cell weight as PHB when grown onglucose/ammonium salts under limiting oxygen. Increasing the availableoxygen leads to a decrease in PHB synthesis and a concomittant reductionin the levels of two of the biosynthetic enzymes. The reduction inenzyme levels is indicative of a regulatory mechanism(s) operating atthe genetic level. Nitrogen limitation of the growth of Alcaligeneseutrophus results in yields of up to 80% dry cell weight PHB. Similarly,Halobacterium and Pseudomonas sp. increase PHB production under nitrogenlimitation.

Under non-limiting conditions, the PHB in organisms that normallyproduce the PHB is rapidly degraded by degradative enzymes. It ispossible to mutate these organisms such that the degradative enzymes areinactive or deleted, hence PHB accumulated during limiting conditions ofgrowth cannot be degraded under non-limiting conditions. In order forthese bacteria to resume growth, the PHB will be excreted into themedium. Alternatively, it is possible to introduce the requisite enzymesinto an organism which does not metabolize PHB (biosynthesis ordegradation) enabling that organism to accumulate large quantities ofPHB under limiting conditions, and when conditions are changed tonon-limiting, the organism should release the PHB into the medium.

By cycling the limiting and non-limiting conditions, it is possible toaccumulate the maximum amount of PHB (based on-absorbance of thebacteria, which increases as a function of polymer content), thenrelease the accumulated polymer into the medium by changing theconditions to non-limiting conditions which stimulate replication of thebacteria. The organisms can be cultured in conventional fermentationsystems for continuous removal of the polymer containing medium withoutdisruption of the bacteria.

Expression in Plants and Production of PEB and PHA Polymers.

As described above with reference to bacterial expression systems, thegenes encoding the thiolase, reductase, and/or the polymerase for PHB orPHA can be expressed in plants of a variety of species to produce thedesired polymeric product. The advantages of such a system areimmediately apparent, decreasing dependence on petroleum-based plastics,and creating an economically useful crop for plants which can grow on avariety of soils.

The first requirement for plant genetic engineering is a system todeliver the foreign DNA to plant tissue. The most popular vectors atthis time are the tumour-inducing (Ti) plasmids of Agrobacteriumtumefaciens, using this bacterium as the agent to deliver DNA byinfection. Plant DNA viruses can also be used as vectors, such asvectors based upon the cauliflower mosaic viruses or the Gemini virusvectors. There are also a number of methods of direct gene transfer toplant cells, including chemically stimulated DNA uptake by protoplasts,electroporation, electroinjection of intact plant cells,liposome-mediated transformation of protoplasts, and DNA transformationby direct injection into plants. Chemically stimulated uptake involvesincubating protoplasts with donor and carrier DNA in the presence of 13%(w/v) polyethylene glycol in 40 mM CaCl₂. Post-incubation is carried outwhereby the PEG concentration is gradually lowered as the CaCl₂concentration is gradually raised. Electroporation is the processwhereby electrical pulses of high field strength are used to reversiblypermeabilize cell membranes to facilitate uptake of large molecules,including DNA. Electroinjection and direct injection have the advantagethat they do not require formation of protoplasts first. These methodsare known to those skilled in the art. See, for example, the review byC. P. Lichtenstein and S. L. Fuller, “Vectors for the geneticengineering of plants”, Genetic Engineering, ed. P. W. J. Rigby, vol. 6,104-171 (Academic Press Ltd. 1987).

The genes can be introduced into the cytoplasm, mitrochondria, orchloroplast, either directly or using targeting sequences. Vectors andtargeting sequences and promoters for plants are known to those skilledin the art and are commercially available from Pharmacia-LKBBiotechnology, 800 Centennial Ave., Piscataway, N.J. 08854-9932, andStragene, La Jolla, Calif.

Any type of plant which produces a useful carbon substrate can beengineered for polymer production. As used with reference to productionof polymers in plants, “polymer” includes PHB, PHA, and novelcarbon-based polymers synthesized from fatty acids using the disclosedpolymerases. If the plant does not form the appropriate fatty acids, thethiolase and reductase genes can be introduced into the plant along withone or more polymerases. The A. eutrophus polymerase polymerizes C4 andC5 substrates. The P. oleovarans polymerase acts on longer substrates,such as C6 to C18 fatty acids, but not short chain fatty acids. Theplants can also be modified, preferably by mutagenesis, to block theglycerol ester and fatty acid degradation pathways so that the plantforms the appropriate substrate.

The genes can be introduced into any type of plant. Cereal plants arepreferred, such as corn, wheat and rice, since they are widely grown andtheir genetic systems are well characterized. Other useful agronomicplants include tobacco and high oil seed plants, especially thosevarieties which grow in desert or in mineralized soil.

The genes can also be introduced into plant cell culture systems, manyof which are known to those skilled in the art. Cell culture of avariety of cereal and other agricultural crops is described in detail inHandbook of Plant Cell Culture vol. 4 edited by D. A. Evans, W. R.Sharp, and P. V. Ammirato (Macmillan Publishing Co. NY 1986). A specificexample of a plant system in which much genetic work has been conductedis Arabidopsis thaliana. Polymer production in cell culture can bemanipulated not only by introduction of the cloned genes but also bevariation in substrates and culture conditions, as described withreference to production in bacteria.

Modifications and variations of the present invention, a method formaking polyhydrbxybutyrate and polyhydroxybutyrate-like polymers havingcarbon-carbon backbones using recombinant engineering according to theforegoing detailed description, and the resulting polymers, will beobvious to those skilled in the art. Such variations and modificationsare intended to come within the scope of the appended claims.

1. A method for constructing polyhydroxylalkanoate polymers andcopolymers in a host comprising: selecting Alcaligenes eutrophus as ahost for expression of genes encoding enzymes required for synthesis ofpolyhydroxyalkanoate polymers and copolymers, introducing into the hostisolated structural genes encoding enzymes selected from the groupconsisting of beta-ketothiolases, acetoacetyl-CoA reductases,polyhydroxybutyrate polymerases, and polyhydroxyalkanoate polymerases incombination with regulatory sequences for expression of the genes in thehost, expressing the enzymes encoded by the introduced genes, andproviding appropriate substrates for the expressed enzymes to synthesizepolyhydroxyalkanoate polymers and copolymers.
 2. (canceled)
 3. Themethod of claim 1 further comprising selecting the enzymes on the basisof their substrate specificity.
 4. The method of claim 1 furthercomprising altering the substrate specificity of the enzymes bymodifying the genes encoding the enzymes.
 5. The method of claim 1further comprising providing regulatory sequences in the expressionvector which control expression of the genes encoding the enzymesrequired for synthesis of polyhydroxyalkanoate polymers and copolymersin response to specific inducers.
 6. The method of claim 5 wherein theinducer is selected from the group consisting of temperature changes andspecific substrate.
 7. (canceled)
 8. The method of claim 1 wherein thehost is deficient in at least one enzyme required for synthesis ofpolyhydroxyalkanoate polymers and copolymers.
 9. (canceled)
 10. Themethod of claim 1 wherein the genes encode enzymes stereospecific forthe D isomer of the Hydroxyacyl-CoA substrate.
 11. Thepolyhydroxyalkanoate produced by the method of claim
 1. 12-27.(canceled)
 28. A system for synthesizing biopolymers having polyesterbackbones comprising selecting Alcaligenes eutrophus as a host forexpression of genes encoding enzymes required for synthesis ofpolyhydroxyalkanoates, introducing into the host isolated structuralgenes encoding enzymes selected from the group consisting ofbeta-ketothiolases, acetoacetyl-CoA reductases, polyhydroxybutyratepolymerases, and polyhydroxyalkanoate polymerases in combination withregulatory sequences for expression of the genes in the host, andproviding appropriate substrates for the enzymes to synthesizepolyhydroxyalkanoates. 29-30. (canceled)